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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# Generating static variables
generate_study_population_static:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static.csv
# Generating static variables
generate_study_population_static_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static_2020 --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2020.csv
# Generates study population for CV - start date = 2018-03-01
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-04-30 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
# Join static and time-varying variables
join_cohorts_cvd:
run: >
cohort-joiner:v0.0.30
--lhs output/measures/input_*.csv
--rhs output/input_static.csv
--output-dir output/measures/cvd
needs: [generate_study_population, generate_study_population_static]
outputs:
highly_sensitive:
cohort: output/measures/cvd/input_*.csv
join_cohorts_cvd_2020:
run: >
cohort-joiner:v0.0.30
--lhs output/measures/input_*.csv
--rhs output/input_static_2020.csv
--output-dir output/measures/cvd/test
needs: [generate_study_population, generate_study_population_static_2020]
outputs:
highly_sensitive:
cohort: output/measures/cvd/test/input_*.csv
# Generates study population for mental health outcomes - start date = 2018-03-01
generate_study_population_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_mh --index-date-range "2018-03-01 to 2022-04-30 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_mh_*.csv
# Join static and time-varying variables
join_cohorts_mh:
run: >
cohort-joiner:v0.0.30
--lhs output/measures/input_mh_*.csv
--rhs output/input_static.csv
--output-dir output/measures/mh
needs: [generate_study_population_mh, generate_study_population_static]
outputs:
highly_sensitive:
cohort: output/measures/mh/input_mh_*.csv
# Check join
#join_check:
# run: stata-mp:latest analysis/variable_check.do
#needs: [join_cohorts_cvd, join_cohorts_mh, join_cohorts_cvd_2020]
#outputs:
# moderately_sensitive:
# log: logs/missing_check.log
# Generates study population for diabetes outcomes
generate_study_population_dm:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-04-30 by month" --output-dir=output/measures/dm --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/dm/input_dm_*.csv
# Generates study population for respiratory outcomes
generate_study_population_resp:
run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-04-30 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/resp/input_resp_*.csv
# Generates study population for mortality
generate_study_population_mortality:
run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-04-30 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/mortality/input_mortality_*.csv
# Generates study populations for baseline tables at 3 timepoints
generate_study_population_tables_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2019-01-01.csv
generate_study_population_tables_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2020-01-01.csv
generate_study_population_tables_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2021-01-01.csv
# Generates baseline tables
create_baseline_tables:
run: stata-mp:latest analysis/101_baseline_tables.do
needs: [generate_study_population_tables_2019, generate_study_population_tables_2020, generate_study_population_tables_2021]
outputs:
moderately_sensitive:
log: logs/table1_descriptives.log
output: output/tables/baseline_table_*.csv
# Generates summary measures for CV
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures/cvd
needs: [join_cohorts_cvd]
outputs:
moderately_sensitive:
measure: output/measures/cvd/measure_*_rate.csv
# Generates summary measures for mental health outcomes
calculate_measures_mh:
run: cohortextractor:latest generate_measures --study-definition study_definition_mh --output-dir=output/measures/mh
needs: [join_cohorts_mh]
outputs:
moderately_sensitive:
measure: output/measures/mh/measure_*_rate.csv
# Generates summary measures for diabetes outcomes
calculate_measures_dm:
run: cohortextractor:latest generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
needs: [generate_study_population_dm]
outputs:
moderately_sensitive:
measure: output/measures/dm/measure_dm_*_rate.csv
# Generates summary measures for respiratory outcomes
calculate_measures_resp:
run: cohortextractor:latest generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
needs: [generate_study_population_resp]
outputs:
moderately_sensitive:
measure: output/measures/resp/measure_*_rate.csv
# Generates summary measures for mortality outcomes
calculate_measures_mortality:
run: cohortextractor:latest generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
needs: [generate_study_population_mortality]
outputs:
moderately_sensitive:
measure: output/measures/mortality/measure_*_rate.csv
# Generates graphs for CVD & mental health outcomes
graphs_mh_cvd:
run: stata-mp:latest analysis/102_graphs_mh_cvd.do
needs: [calculate_measures, calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/graphs_mh_cvd.log
output: output/graphs/line_*.svg
# Generates graphs for diabetes outcomes
graphs_dm:
run: stata-mp:latest analysis/103_graphs_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/graphs_dm.log
output: output/graphs/line_dm_*.svg
# Generate graphs for respiratory outcomes
graphs_resp:
run: stata-mp:latest analysis/104_graphs_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/graphs_resp.log
output: output/graphs/line_resp_*.svg
# Generate graphs for mortality
graphs_mortality:
run: stata-mp:latest analysis/105_graphs_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/graphs_mortality.log
output: output/graphs/line_mortality_*.svg
# Running analysis scripts
model_checks_dm:
run: stata-mp:latest analysis/201_model_check_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/model_checks_dm.log
output: output/time_series/dm_*.svg
model_checks_resp:
run: stata-mp:latest analysis/202_model_check_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/model_checks_resp.log
output: output/time_series/resp_*.svg
model_checks_cvd:
run: stata-mp:latest analysis/203_model_check_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/model_checks_cvd.log
output: output/time_series/cvd_*.svg
model_checks_mh:
run: stata-mp:latest analysis/204_model_check_mh.do
needs: [calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/model_checks_mh.log
output: output/time_series/mh_*.svg
model_checks_mortality:
run: stata-mp:latest analysis/205_model_check_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/model_checks_mortality.log
output: output/time_series/mortality_*.svg
time_series_resp:
run: stata-mp:latest analysis/206_time_series_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/tsreg_resp.log
output: output/time_series/tsreg_resp*.csv
graph: output/time_series/margins_resp*.svg
time_series_dm:
run: stata-mp:latest analysis/207_time_series_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/tsreg_dm.log
output: output/time_series/tsreg_dm*.csv
graph: output/time_series/margins_dm*.svg
time_series_cvd:
run: stata-mp:latest analysis/208_time_series_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/tsreg_cvd.log
output: output/time_series/tsreg_cvd_*.csv
graphs: output/time_series/margins_cvd*.svg
time_series_mh:
run: stata-mp:latest analysis/209_time_series_mh.do
needs: [calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/tsreg_mh.log
output: output/time_series/tsreg_mh*.csv
graphs: output/time_series/margins_mh*.svg
time_series_mortality:
run: stata-mp:latest analysis/210_time_series_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/tsreg_mortality.log
output: output/time_series/tsreg_mortality*.csv
graph: output/time_series/margins_mort*.svg
# Study definition for pre-pandemic survival analysis
generate_study_population_survival_pre:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_pre --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_pre*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_pandemic:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_pandemic --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_pandemic*.csv
# Study definition for pandemic waves
# Using dates: wave 1 2020-03-23 to 2020-05-30, wave 2 2020-09-07 to 2021-04-24, wave 3 2021-05-28 to 2021-12-14
# Easing period after each wave
# dates match covid_mortality_over_time study - wave 1 & 2 based on ONS COVID infection survey, wave 3 based on >50% prevalence
generate_study_population_survival_wave1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_wave1 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_wave1*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_easing1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_easing1 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_easing1*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_wave2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_wave2 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_wave2*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_easing2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_easing2 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_easing2*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_wave3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_wave3 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_wave3*.csv
# Study definition for pandemic survival analysis
generate_study_population_survival_easing3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_survival_easing3 --output-dir=output/survival --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/survival/input_survival_easing3*.csv
# Cox models
# Perpare datasets
cox_model_prep:
run: stata-mp:latest analysis/301_cox_model_prep.do
needs: [generate_study_population_survival_pre, generate_study_population_survival_pandemic, generate_study_population_survival_wave1, generate_study_population_survival_easing1, generate_study_population_survival_wave2, generate_study_population_survival_easing2, generate_study_population_survival_wave3, generate_study_population_survival_easing3]
outputs:
highly_sensitive:
output: output/prep_survival*.dta
moderately_sensitive:
log: logs/cox_model_prep.log
# Check data
cox_data_check:
run: stata-mp:latest analysis/301_1_variable_check.do
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/variable_check.log
# Repeat for each outcome
cox_models_cvd:
run: stata-mp:latest analysis/302_cox_models.do "cvd"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_cvd.log
output: output/tables/cvd*.txt
graph: output/graphs/km_cvd*.svg
cox_models_mi:
run: stata-mp:latest analysis/302_cox_models.do "mi"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_mi.log
output: output/tables/mi*.txt
graph: output/graphs/km_mi*.svg
cox_models_stroke:
run: stata-mp:latest analysis/302_cox_models.do "stroke"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_stroke.log
output: output/tables/stroke*.txt
graph: output/graphs/km_stroke*.svg
cox_models_heart_failure:
run: stata-mp:latest analysis/302_cox_models.do "hf"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_hf.log
output: output/tables/hf*.txt
graph: output/graphs/km_hf*.svg
cox_models_vte:
run: stata-mp:latest analysis/302_cox_models.do "vte"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_vte.log
output: output/tables/vte*.txt
graph: output/graphs/km_vte*.svg
cox_models_t1dm:
run: stata-mp:latest analysis/302_cox_models.do "t1dm"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_t1dm.log
output: output/tables/t1dm*.txt
graph: output/graphs/km_t1dm*.svg
cox_models_t2dm:
run: stata-mp:latest analysis/302_cox_models.do "t2dm"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_t2dm.log
output: output/tables/t2dm*.txt
graph: output/graphs/km_t2dm*.svg
cox_models_dm_keto:
run: stata-mp:latest analysis/302_cox_models.do "dm_keto"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_dm_keto.log
output: output/tables/dm_keto*.txt
graph: output/graphs/km_dm_keto*.svg
cox_models_dm:
run: stata-mp:latest analysis/302_cox_models.do "dm"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_dm.log
output: output/tables/dm*.txt
graph: output/graphs/km_dm*.svg
cox_models_asthma:
run: stata-mp:latest analysis/302_cox_models.do "asthma"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_asthma.log
output: output/tables/asthma*.txt
graph: output/graphs/km_asthma*.svg
cox_models_copd:
run: stata-mp:latest analysis/302_cox_models.do "copd"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_copd.log
output: output/tables/copd*.txt
graph: output/graphs/km_copd*.svg
cox_models_depress:
run: stata-mp:latest analysis/302_cox_models.do "depress"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_depress.log
output: output/tables/depress*.txt
graph: output/graphs/km_depress*.svg
cox_models_anx:
run: stata-mp:latest analysis/302_cox_models.do "anx"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_anx.log
output: output/tables/anx*.txt
graph: output/graphs/km_anx*.svg
cox_models_smi:
run: stata-mp:latest analysis/302_cox_models.do "smi"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_smi.log
output: output/tables/smi*.txt
graph: output/graphs/km_smi*.svg
cox_models_mh:
run: stata-mp:latest analysis/302_cox_models.do "mh"
needs: [cox_model_prep]
outputs:
moderately_sensitive:
log: logs/cox_model_mh.log
output: output/tables/mh*.txt
graph: output/graphs/km_mh*.svg
cox_models_graphs:
run: stata-mp:latest analysis/303_cox_models_graphs.do
needs: [generate_study_population_survival_pre, generate_study_population_survival_pandemic]
outputs:
moderately_sensitive:
log: logs/cox_model_graphs.log
graph: output/survival/estimates_*.svg